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Cowen & Company 29th AnnualHealthcare Conference

Kevin HrusovskyPresident & CEO

March 17, 2009

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This presentation includes forward-looking statements, including financial projections. Reference to what we expect, believe, intend to do, plan, hope, estimate or other statements referring to future events or results are intended to identify those as forward-looking statements. Forward-looking statements are inherently subject to risks and uncertainties. Further information on risks faced by Caliper are included under the caption Factors Affecting Operating Results in Caliper's annual report on Form 10-K, filed with the Securities and Exchange Commission on March 13, 2009. Caliper’s SEC filings are available on the website maintained by the Securities and Exchange Commission at www.SEC.gov. Caliper does not undertake any obligation to update forward-looking or other statements in this presentation to reflect any change in Caliper's expectations with regards to such statements or any change in events, conditions or circumstances on which any such statements are based.

This presentation includes certain non-GAAP measures. Reconciliations of the Non-GAAP Financial Measures used herein appear at the end of this presentation.

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BusinessTools to accelerate pre-clinical research and enable MdxInstruments, services and technology (I. robotics, II. chips, III. imaging)

StrategyCommercialize technologies into attractive “disease” models and Mdx platforms

LocationsCorporate: Boston; R&D: S.F. Bay Area; Services: East coast; Sales: Global

FinancialNASDAQ CALP 2008 revenue - $134.1M GAAP; $122.8M ProForma(after divestitures)

55% Pharma; 35% Acad/Gov’t; 10% Biotech65% Americas; 35% ROW

Caliper at a Glance

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Substantially Improved outlook with enhanced balance sheet, top line growth, cost reductions, recurring revenue and patent protection

Significant Q4 momentum with completed divestitures and sharpened SBU focus

Achieved $36.7 M Q4’08 revenue, at top end of guidance

Delivered positive ebitda in Q4’08 for the second quarter in a row, despite eliminated earnings of divested businesses

Enhanced balance sheet: Sep’08 Now

- Total available cash $15M $35M

- Net cash ($6M) $12M

- Loan due date Jun’09 Nov’10

Launched IVIS Kinetic in second half 2008, strengthening IVIS leadership

Strong growth in molecular application markets, led by new LabChip Gx with 26 Q4 placements and 70% growth to Q4’07. 40 units placed in 2nd half.

Reduced costs $12M in 2008, lowering breakeven Ebitda revenue from $155M to $138M; Targeting Ebitda breakeven revenue of $132M by year end 2009

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Strategy

Assemble “tool box” of leading technologies for Research and Mdx

Sharpen focus on molecular applications and recurring profitable growth

The Microfluidics Company The Applications Company- Instruments- Chips- IP

- Drug development and molecular diagnostics - Molecular applications (plates, chips, animals)- LabChip and imaging platforms

2003 2009

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$1B / 15 years

DNA, RNA, Protein Cells Mice Tissue Humanin vitro in vivo

Strategic TransformationAssemble “tool box” of leading technologies for Research and Mdx

Research

$57M ’08

4% mkt growth

Imaging

$46M ’08

12% mkt growth

Services

$20M ’08

10% mkt growth

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Historic and Projected Growth (GAAP)

-60

-40

-20

0

20

40

60

80

100

120

140

160

180

200

220

2002 2003 2004 2005 2006 2007 2008 2009E

Rev

enue

& E

BIT

DA

$M

illion

s .

Total RevenueContract & Licens e

2002 2003 2004 2005 2006 2007 2008 2009E

Revenue & EBITDA Outlook

2009 Assumptions

Organic growth midpoint 5.5%65% revenue patent protected15% R&D investmentEbitda breakeven $138M Q1 -$132M yr endApproaching Ebitda breakeven$35M available cash Jan’09Project $25M+ cash at year end ‘09

Total RevenueuF Contract & LicenseEBITDARevenue from Divested Operations

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Strategic Road MapSharpen focus on molecular applications and recurring profitable growth

0 $200 M $600 M $1 B+

5%

10%

0%

20%

15%

$400 M $800 M

ResearchReconfigure

$57 ‘08

ResearchReconfigure

$57 ‘08Non Core Products

Non Core Products

ImagingMarket Expansion

$46M ‘08

ImagingMarket Expansion

$46M ‘08

ServicesShare Gain

$20M ‘08

ServicesShare Gain

$20M ‘08

Mar

ket G

row

th R

ates

Market Size

Molecular ApplicationsMolecular

Applications

Shed

Gro

w

New Diseases and ModalitiesNew Diseases and ModalitiesExpand

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Strategic ReconfigurationEnhance Growth and profitability through SBU focus

2008 2009SBU Organic Growth Organic Growth

Research Products 4% 4%

Imaging 13% 10%

Services -6% 4%

Total Revenue 6% 6%

Note: Organic growth percentages exclude PDQ, AutoTrace, deferred revenue adjustments in purchase accounting and 2007 one time license and contract revenues in microfluidics. It also excludes adjustments for expected/actual foreign exchange effects.

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Strategic ReconfigurationEnhance Growth and profitability through SBU focus

Q1 '09SBU Organic Growth

Research Products 10%

Imaging 3%

Services -18%

Total Revenue 3%

Note: Organic growth percentages exclude PDQ, AutoTrace, deferred revenue adjustments in purchase accounting and 2007 one time license and contract revenues in microfluidics. It also excludes adjustments for expected/actual foreign exchange effects.

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Strategic Reconfiguration

SBU Offering08-'09Units

2009Revenue

Organic RevenueGrowth

Research Molecular LH Platforms Molecular LC PlatformsShed Non-core Products

45 - 80+ 62 - 100+

$4.5 M$5.5 Mt.b.d.

75%40%

Imaging IVIS Platforms (incl. Kinetic) 143 - 160 $30 M 12%

Services EPAPfizerWyeth

$3 M$2 M$1 M

200%20%50%

Asia Molecular Application & IVIS $15 M 15%

Enhance Growth and profitability through SBU focus

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Research: LabChip® Instruments and Chips

BenefitsHigh Data QualityImproved SensitivityReduced CostsImproved Productivity

FeaturesMiniaturizationIntegrationAutomation

0

25

50

75

100

125

150

175

200

225

250

275

300

2000 2001 2002 2003 2004 2005 2006 2007 2008

Over 300 Cumulative LabChip Installations

Direct Channel Instrument Placements

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Research: Existing Microfluidics Applications

Separations:• Fast runs• Automated • Digital Data quality

Application areas:• Genomics research

• Sequencing• Gene expression

• Protein purification• Antibody QC

Low throughput7000 units installed

LabChip® GX I & II

Kinase profiling• Bench top compound

screening• 200 kinases available

System includes:• Reader• Reagents (ProfilerPro plates)

Potential for other enzymatic assays

=LabChip® EZ Reader

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LabChip® is Superior to Manual Methods

• 60 X faster: Seconds vs minutes or hours• 4 X less steps: Automated vs labor intensive manual• 10-20 X less sample: 1ul vs 10-20 ul sample• High quality data: Quantitative SW analysis vs qualitative bands• Digital data: File sharing & archiving vs dried gel

LabChip® GX I & II46 sold in 2nd H’0885+ expected in 2009

Manual Gel Approach

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Q4 & Q1 LabChip GX PurchasesCustomers purchasing LabChip for:

– Protein therapeutics (Antibody) labs– Molecular biology laboratories– University core facilities– Molecular diagnostic reference laboratories– Reagent manufacturers– Contract manufacturing organizations– National government laboratories

Many companies acquiring multiple unitsAsia companies not represented (distribution)

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March 11th Cambridge Symposium75 registered attendeesKey highlights:

– LabChip GX highly touted for protein PAT/QbD and molecular biology applications

– Process analytics for protein therapeutics is an attractive market with significant long term growth potential

– LabChip GX enables experiments in an afternoon that require a month using CE

– GX coupled with statistical DOE methods yields faster time to biomass production

Sampling of attendees:

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Molecular biology workstation

DNA fractionation for Nex Gen Seq’n

Mdx applicationsProtein, Dna and RnaPOC, faster, lower cost and less samplePartner launching immunoassay panel for liver cancer on a plastic chip this year

Pipeline of Next Gen Molecular Applications

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Conversion of Liver Cancer Assay to Chip Based Format

Existing FDA approved clinical analyzer based Immuno assay

Plastic chip based immuno- assay

$4$10Cost per test (approx)

1pM (0.1ng/mL)5 to 11 pMSensitivity

100 seconds30 minutesTime per sample

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LabChip Based Immuno-Assay Format

• High Sensitivity – 0.1 to 1pM on chip sensitivity– 1pM to 5pM detection of analytes directly in serum

• Assay parameters – Picomolar to nanomolar detection capabilities – Range of 104

– In-line dilution to extend range– Assay precision 2% to 3% CVs

• Rapid convenient testing– Individual assays in as little as 90 seconds– Small desktop instrument platform– Multiplex analyte detection capabilities

• Minimal sample requirements– 5 to 50 microliters of sample– Analyte concentration capabilities (200x)– Can resolves protein iso-forms

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Platform Overview

IVIS Lumina II - $120k

• Entry-level optical imaging

• Flexible and expandable with options and accessories

• Calibrated for quantitative longitudinal studies

IVIS Kinetic - $170k5 sold in Q4’08

• Fast and conventional imaging in one system

• Calibrated for quantitative longitudinal studies

• Characterization of real-time event monitoring

• Improved gross margin

IVIS Spectrum - $330k>125 Sold ~ $40M

• Total optical imaging package in one system

• Absolute quantitation independent of location and size of source

• 3D visualization

• Improved gross margin

New 2007

Imaging:

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Imaging: IVIS Revenue History($M’s)

0.05.0

10.015.020.025.030.035.040.045.0

2002 2003 2004 2005 2006 2007 2008

LicenseProduct

Units Sold/YearInstalled Base

3262

44106

82188

97285

120405

132537

Addressable Market*

5,000+ units143680

Source: Company estimates

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Imaging: IVIS Imaging SystemsNon-invasive in vivo Imaging

• Oncology• Infectious Disease• Inflammation• Metabolic Diseases• Neurology• Gene Therapy• Stem cell Biology• Cardiovascular Disease• Immunology & Transplantation Biology

Over 700 publications establish IVIS as the leading optical imaging platform for bioluminescence and fluorescence applications

0

50

100

150

200

250

95 96 97 98 99 00 01 02 03 04 05 06 07

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Imaging: Therapeutic Expansion - Models and Applications

CNS - Stroke ModelsGFAP-Luc

Oncology - Spontaneous tumor modelEL1-Tag- Luc

Metabolic Disease – Diabetes modelRIP-Luc

Inflammation – Arthritis modelFluorescent conjugate detects

Thrombin activity

Primate Models – Viral gene transferMacaque Model

Stem Cells – grafting ofNeuronal stem cells

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Imaging: Advance made in sensitivity of optical imaging agents

Detection limit107 to 106 cells

PETFDG-glucose probe

IVISLuc labeled tumor cells

Detection limit1-2 cells

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• Conscious animal applicationsReal-Time Fast ImagingEvent and Moving Object Tracking

• Anesthetized – real time functional eventsPerfusion dynamics

– Vascular properties within tumors and organsFlash Events

– Calcium and membrane potential transientsCompound distributionImmunological ReactionsPharmacokinetics/ Pharmacodynamics

Imaging: The Biology

Real-Time Fast Optical Imaging

Kinetic

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EPA ToxCast Contract UpdateCALP awarded two to five year contract in 2007 for $1.4M - $69M; Contract-to-date revenue is $3.5M and anticipate $3M in 2009, starting Q3

CALP screened 320 compounds in 239 in vitro assays as the first step to build a database for predicting in vivo toxicity of environmental chemicals.

EPA scientists reporting initial analyses of Caliper screening data at national toxicology meetings being held this week

• High quality data and preliminary links to in vivo toxicity shown

EPA optioned the third year of contract two weeks ago

EPA is releasing early findings reinforcing project focus

EPA will release more extensive analysis of data in mid-May

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Strategic Transformation

SBU Long-term Impact

Research Plastic ChipLabChip NextGenHand Held POC Dx

New economics - Game changing technologyExpand into nextgen sequencing/sample PrepAssessing content / collabortion oppt's

Imaging New Modalities - R&D - Acquisition

Market expansion (x-ray, CT, etc.)Leverage leadership position

Services EPA, Other Pharma / BioTech Increase gross marginCapitalize on outsourcing trend

Refine Channel Exploring Channel Alternatives Increase mkt penetration and grow Asia

Sharpen focus on attractive applications and recurring profitable growth

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A Compelling Inflection PointSummary

Exciting product portfolio with 65% of revenue IP protected and focused on robust molecular applications and emerging molecular diagnostic applications

Strong growth momentum with ’08 product launches; Ivis imagers, LabChip GX / EZReader, Genomic Workstation and EPA Toxcast. Guiding positive growth in ’09.

Two consecutive qtr’s positive Ebitda and anticipate positive Ebitda in the 2nd half of 2009 and full year 2010. Breakeven revenue now targeted at $132M by ‘09 year end

Enhanced balance sheet; $27M cash on hand and $8M additional debt capacity on Jan 1, 2009

Additional opportunity to shed small products to fund organic and acquisition growth

Secured IP and evolving plan to convert microfluidics to “game changing” plastic chip technology to enable increased margins and molecular diagnostic applications

Metrics:• 2009 revenue guidance $125M - $129M (4 - 7% organic growth)• Q1’09: $25M - $28M (midpoint is 3% organic growth)

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Non-GAAP Financial MeasuresSchedule I - EBITDA Reconciliation for the years ended December 31, 2002 through 2008 (In thousands)

2002 2003 2004 2005 2006 2007 2008 Notes

GAAP Operating Loss (46,637)$ (52,843)$ (32,542)$ (14,549)$ (29,985)$ (23,828)$ (69,531)$

Adjustments-Depreciation & amortization 5,795 10,169 10,020 7,138 12,730 13,914 11,878 (1) Goodwill impairment - - - - - - 43,365 (2) Employee stock-based compensation 378 1,000 2,770 1,585 5,570 5,161 3,580 (3) Restructuring and severance charges 314 11,535 6,018 (1,005) 258 1,343 5,889 (4) Purchase accounting adjustments - - - - 1,876 1,038 23 (5)

Total Adjustments 6,487 22,704 18,808 7,718 20,434 21,456 64,735

EBITDA (Non-GAAP) (40,150)$ (30,139)$ (13,734)$ (6,831)$ (9,551)$ (2,372)$ (4,796)$

Use of Non-GAAP Financial Measures:

Notes to Schedule I(1) Depreciation and amortization charges related to long-lived tangible assets and amortizable intangible assets.(2) Goodwill impairment related to annual assessment in accordance with SFAS No. 142.(3) Non cash stock based compensation expense charges recognized in accordance with SFAS No. 123R.(4) Restructuring and severance charges related to acquistions, workforce reductions and facility closures undertaken by management

to control costs and improve the focus of its operations in order to reduce losses.(5) Deferred revenue and cost adjustments recorded in purchase accounting that reduce revenues and costs that would otherwise

be recognized on a continuing GAAP basis.

Caliper uses non-GAAP financial measures to supplement financial results which are presented on a GAAP basis. Caliper's management believes that these non-GAAP financial measures provide useful information to investors and others in understanding and evaluating our results.

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GAAPNon-

GAAP2008 2007 2008 2007 2008 2007 % Chg % Chg

- (1) (179) (2) (2,114) (2) (3,964)

Research 17,630$ 20,471$ (2,114)$ (4,143)$ 15,516$ 16,328$ -14% -5%Imaging 14,383 14,715 - (3) 20 14,383 14,735 -2% -2%Services (CDAS) 4,682 5,070 - - 4,682 5,070 -8% -8%

Total revenue 36,695 40,256 (2,114) (4,123) 34,581 36,133 -9% -4%

GAAPNon-

GAAP2008 2007 2008 2007 2008 2007 % Chg % Chg

- (1) (11,217) (2) (11,308) (2) (15,492)

Research 68,519$ 80,673$ (11,308)$ (26,709)$ 57,211$ 53,964$ -15% 6%Imaging 45,765 39,084 (3) 23 (3) 1,037 45,788 40,121 17% 14%Services (CDAS) 19,770 20,950 - - 19,770 20,950 -6% -6%

Total revenue 134,054 140,707 (11,285) (25,672) 122,769 115,035 -5% 7%

GAAP

Three Months Ended December 31,

GAAP

Year Ended December 31,

Non-GAAP Adjustments

Non-GAAP Adjustments

Non-GAAP

Non-GAAP

Notes to Schedule II:

For purposes of comparing growth rates for each of the three principal areas of Caliper’s business, the above non-GAAP table reconciliation excludes the following:

(1) Reflects elimination of certain collaboration-related microfluidic license and contract revenue recognized during the three and twelve-months ended December 31, 2007 which were concluded in 2007.

(2) Reflects elimination of the revenues related to the PDQ and AutoTrace product lines divested in November 2008.

(3) Reflects the add back of the deferred revenue adjustments recorded in purchase accounting that reduce revenues that would otherwise be recognized on a continuing GAAP basis.

We believe this is a useful measure in evaluating revenue performance among comparative periods, but these non-GAAP comparisons are not intended to substitute for GAAP financial measures.

Non-GAAP Financial MeasuresSchedule II – Reconciliation of Non-GAAP Revenue Comparison for the Three and Twelve Months Ended December 31, 2008